In the chat it is possible to reply to a specific message, and it is easy to follow to which message it was replied.
In the comments to answers, it is difficult to tell to which comment another comment is reply to. It would be great to add the same functionality for comments as for the chat.
There's a userscript for that :) It's not perfect, but it goes a lot of the way to doing what you want. Don't forget to vote up the script instead of this answer
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After:
In the comments to answers, it is difficult to tell to which comment another comment is reply to.
This is, for the most part, intentional.
We suppress comment discussion in favor of questions and answers.
As a moderator, I would really like this to be implemented. This would make it a lot easier to follow the flow of a discussion, particularly to evaluate its context and civility. Case in point, I recently came across a comment including "@user - so you're here to bicker?" and it would be much easier to see whether the accused user is out of line if we had highlighting of the pinged user's messages.
